Shedninja is... not useless per se, but incredibly awkward.
Anything rock-type is going to have a hard time
Ditto wastes a turn transforming and is no better than its opponent for it.
Wild cocoon monsters have no damaging moves.
Unown are plot-devices unworthy of anything beyond collection.
Bidoof is to Shinō what Rattata is to Kanto, thus redundant.
Abra can only teleport (or has this changed?).
So on, so forth. I'm not going to spend my entire day listing these things; they're usually obvious enough.
But I'd like to say, while Zubat is annoying in its abundance, it's far from useless. Confuse ray, screech, bite — great little thing.